[Bioperl-l] Error calling alignment method

Wed Jun 1 15:37:43 UTC 2011

Chris,
I just downloaded and installed Bioperl 1.6.901 and... everything is 
working fine now!!!
Thank you very much,
Lorenzo

El 01/06/11 15:31, Chris Fields escribió:
> I think Dave made some changes after 1.6.1; try upgrading to the latest version on CPAN (1.6.901):
>
> http://search.cpan.org/~cjfields/BioPerl-1.6.901/
>
> chris
>
> On Jun 1, 2011, at 5:52 AM, Lorenzo Carretero Paulet wrote:
>
>> perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"' : 1.006001
>> Thanks,
>> Lorenzo
>> El 01/06/11 12:17, Roy Chaudhuri escribió:
>>> Again, works fine for me (after changing the file and directory locations, and uncommenting the subroutine calls). Which Bioperl version are you using?
>>>
>>> On 31/05/2011 20:04, Lorenzo Carretero Paulet wrote:
>>>> Thanks for the reply,
>>>> I attach again the revised versiont of the script I'm working with as
>>>> well as the sequences. I still have the same error. The funny thing is
>>>> that the yn00 subroutine is running properly when the alignment is
>>>> passed directly, but not the codeml one (using either PAML 4.2 or 4.4).
>>>> However, both PAML versions and programs are working fine with my data
>>>> when I ran them manually.
>>>> Any suggestion will be much appreciated.
>>>> CHeers,
>>>> Lorenzo
>>>>
>>>>    and El 31/05/11 19:28, Roy Chaudhuri escribió:
>>>>> Hi Lorenzo,
>>>>>
>>>>> I tried your code (the one you attached as testa.pl), and the only
>>>>> errors that were reported were unininitialized values $Ka at lines 90
>>>>> and 150 when you print the output. This is because of typos in your
>>>>> script, you have "dA" instead of "dN" (PAML uses the terms "dN" and
>>>>> "dS" for Ka and Ks, respectively).
>>>>>
>>>>> I can only think that the problem you are experiencing is because of
>>>>> some change to the PAML output format (although it worked fine for me
>>>>> with a just-downloaded PAML4.4 and an older PAML4). From what I
>>>>> recall, PAML always did have quite volatile output formats. Older
>>>>> versions of PAML are archived, so you could try downgrading:
>>>>> http://abacus.gene.ucl.ac.uk/software/pamlOld.html
>>>>>
>>>>> Cheers,
>>>>> Roy.
>>>>>
>>>>> On 25/05/2011 23:23, Lorenzo Carretero wrote:
>>>>>> Dave, Jason:
>>>>>>
>>>>>> I had already tried running PAML manually with the alignment (I always
>>>>>> do this to confirm software is properly installed and set up), and ran
>>>>>> again with an edited version of the alignment removing the stop codons
>>>>>> (I didn't know stop codons at the ends of the alignmente could affect
>>>>>> PAML, but inframe stop codons). It worked properly in both cases. I ran
>>>>>> again my script (see attached testa.pl) using two different methods, one
>>>>>> constructing the codon alignment using aa_to_dna_aln and another one
>>>>>> passing the aligned sequences (in both cases after removing the stop
>>>>>> codons). I had again the message:
>>>>>>
>>>>>> ------------- EXCEPTION: Bio::Root::NotImplemented -------------
>>>>>> MSG: Unknown format of PAML output did not see seqtype
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw /Library/Perl/5.10.0/Bio/Root/Root.pm:368
>>>>>> STACK: Bio::Tools::Phylo::PAML::_parse_summary
>>>>>> /Library/Perl/5.10.0/Bio/Tools/Phylo/PAML.pm:461
>>>>>> STACK: Bio::Tools::Phylo::PAML::next_result
>>>>>> /Library/Perl/5.10.0/Bio/Tools/Phylo/PAML.pm:270
>>>>>> STACK: main::GettingBioperlAlignmentAAtoDNAplusPAMLcalculation
>>>>>> /Users/Lorenzo/Documents/workspace/PlantEvolGen/testa.pl:83
>>>>>> STACK: /Users/Lorenzo/Documents/workspace/PlantEvolGen/testa.pl:23
>>>>>> ----------------------------------------------------------------
>>>>>>
>>>>>> Thanks,
>>>>>> Lorenzo
>>>>>>
>>>>>> On 5/25/11 10:24 PM, Jason Stajich wrote:
>>>>>>>> ------------------------------------------
>>>>>>>>
>>>>>>>> I think the codon alignment is being proberly constructed by the
>>>>>>>> method aa_to_dna_aln, as I can do a Dumper printing of it. So the
>>>>>>>> problem must be in the PAML codeml wrapper not properly recognizing
>>>>>>>> the codon alignment. Could it be related to the alignment format
>>>>>>>> (PAML runs on PHYLIP formatted files)?
>>>>>>> The writing out in phylip format is taking care of by the factory -
>>>>>>> you are passing in an alignment object so that is not typically the
>>>>>>> problem.
>>>>>>>
>>>>>>> I would repeat Dave's idea that you just dump the codon alignment
>>>>>>> file out and you run PAML manually with it.  The parsing error
>>>>>>> sounds like there are problems when running PAML and you may want to
>>>>>>> check that you don't have stop codons in your alignment.  It looks
>>>>>>> like your CDS file has stops as the last codon so if you drop those
>>>>>>> last 3 bases, how does it work?
>>>>>>>
>>>>>>>> Cheers,
>>>>>>>> Lorenzo
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> -- 
>>>>>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>>>>>>>>
>>>>>>>> Lorenzo Carretero Paulet
>>>>>>>> Institute for Plant Molecular and Cell Biology - IBMCP (CSIC-UPV)
>>>>>>>> Integrative Systems Biology Group
>>>>>>>> C/ Ingeniero Fausto Elio s/n.
>>>>>>>> 46022 Valencia, Spain
>>>>>>>>
>>>>>>>> Phone:  +34 963879934
>>>>>>>> Fax:    +34 963877859
>>>>>>>> e-mail: locarpau at upvnet.upv.es
>>>>>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>>>>>>>>
>>>>>>>>
>>>>>>>> <test_vs_test.par.nt.1.fas><test_vs_test.par.aa.1.fas><code.pl>_______________________________________________
>>>>>>>>
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>>>>>>
>>>>>>
>>>>>>
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>>>>
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>>
>> -- 
>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>> Lorenzo Carretero Paulet
>> Institute for Plant Molecular and Cell Biology - IBMCP (CSIC-UPV)
>> Integrative Systems Biology Group
>> C/ Ingeniero Fausto Elio s/n.
>> 46022 Valencia, Spain
>>
>> Phone:  +34 963879934
>> Fax:    +34 963877859
>> e-mail: locarpau at upvnet.upv.es
>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>>
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>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
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-- 
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
Lorenzo Carretero Paulet
Institute for Plant Molecular and Cell Biology - IBMCP (CSIC-UPV)
Integrative Systems Biology Group
C/ Ingeniero Fausto Elio s/n.
46022 Valencia, Spain

Phone:  +34 963879934
Fax:    +34 963877859
e-mail: locarpau at upvnet.upv.es
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*